August 2021 - ChimeraX-users - RBVI Mailing Lists

ChimeraX File Error :: .vdb File Not Recognized
by Olivia Leland 24 Aug '21

24 Aug '21

Hello, I’m trying to upload a .vdb file from the Virus Particle Explorer databank. To my understanding, I should be able to upload a .vdb file for visualization. Every time I try to open said file, however, it returns the error: Is there a setting I haven’t activated in order to upload this file properly? Additionally, I’m unable to connect the software to the internet so I can’t use File>Fetch By ID... (it won’t show up for me) Do you have any suggestions on how to fix this? Best, Olivia Leland (she/her) Doctoral Student || Fraden Lab Martin A. Fisher School of Physics Brandeis University Waltham, MA 02453

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identifying surface residues
by Elaine Meng 23 Aug '21

23 Aug '21

On Aug 23, 2021, at 2:54 PM, Brian Yang <by2289(a)columbia.edu> wrote: > > Dear Dr. Meng, > I hope you are doing well. My name is Brian. I am a senior at Columbia University. I am currently doing research at the Columbia University Medical Center. I am contacting you because I have a few questions about using Chimera X. > > I am trying to use Chimera X to identify surface residues on a protein. [...] > > I have been looking through the Chimera API, and I found this method that I think could work: > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html > > However, I'm not able to figure out how to do the Attribute Calculator in Chimera X, nor am I able to get the SES area. > > I saw your response in this email chain: > https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-September/001484.ht… > > and I have tried it, but this is only for SAS area. > > So my questions are: > Do you think the surfnorm method is appropriate? If so, how would I achieve the Attribute Calculator functionality in Chimera X? If not, could you give me a better approach to remove these surface residues? > > Thank you for your time! > > Kind regards, > Brian Yang > Hi Brian! For asking questions about ChimeraX, we recommend using the address chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time) unless you are including something that needs to remain private. I edited out some details about your project above just in case. ChimeraX does not calculate solvent-excluded surface area (SESA) nor does it have an Attribute Calculator tool. However, if all you want to do is to identify which residues are on the surface, you could: (1) calculate solvent-accessible surface area (SASA) per residue. Command "measure sasa protein setAttribute true" or something like that. The "protein" part is that so waters, ligands, etc. are not enclosed in the calculated surface. The "setAttribute true" part assigns values to a residue attribute named "area" so that you can do the next step, although it could be omitted since it is already true by default. There are various other options too. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> (2) delete all residues with SASA greater than some value. You wouldn't be normalizing to a percentage exposed since we don't have the values to use for the denominator, but just the raw amount of solvent-accessible area. So you may want to tinker around with what value of the cutoff gives you reasonable results. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> Example: open 4hvp measure sasa protein setAttribute true show hide ~protein hide ribbons sel ::area>20 color sel red color ~sel white ~sel ... see what you think, or try some other value... sel ::area>15 color sel red color ~sel white ~sel When you figure out what value you want to use, you could delete those residues, e.g. delete ::area>15 ...or if you're not sure what to use as a single cutoff and may want to process several times at different cutoffs, you can just write out all of the residues and their area values to an "attribute file"... see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> However, if you really need a % exposure value normalized to account for different residue sizes, you would need to stick with Chimera, at least for now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Labelling w.r.t Residue description
by Gupta, Arun 23 Aug '21

23 Aug '21

Dear ChimeraX team, How can we label the PDB structure in ChimeraX based on the selection as well as "description or residue type". I tried the specific "residues selection" for a PDB structure first and then typed the following command "label @ca residues attr residuename". I could get the residue numbering for the selected residues. But, I failed to get the residue description for the specific selected residues such as "residue 59 should be labelled as His59". Also, I noticed the "size " of the residue numbers "label " is bit small. How can we increase the " font size" ? Please find attached pic. Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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ChimeraX for Windows 10 Not Starting
by Mason Long 20 Aug '21

20 Aug '21

Hi, We're having problems getting ChimeraX to run on Windows 10 21H1. Each time we try running it, the cursor spins for a second or so and then nothing happens. I checked the Event Viewer and see every time we try running it an error event shows up in the Windows Application Error Event Log. Here's the output that shows up in the log for each of those versions: ---------------------------------------- Faulting application name: ChimeraX.exe, version: 1.2.5.0, time stamp: 0x60ab2a1d Faulting module name: Qt5WebEngineCore.dll, version: 5.15.2.0, time stamp: 0x5fad38ab Exception code: 0x80000003 Fault offset: 0x000000000014baff Faulting process id: 0x2b14 Faulting application start time: 0x01d795f43b7d3176 Faulting application path: C:\Program Files\ChimeraX 1.2.5\bin\ChimeraX.exe Faulting module path: C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\PyQt5\Qt\bin\Qt5WebEngineCore.dll Report Id: db7d3af7-6986-47ed-ba27-3ce5e6bfcbae Faulting package full name: Faulting package-relative application ID: ---------------------------------------- Faulting application name: ChimeraX.exe, version: 1.1.0.0, time stamp: 0x5f5afaf7 Faulting module name: Qt5WebEngineCore.dll, version: 5.12.9.0, time stamp: 0x5ee3364a Exception code: 0x80000003 Fault offset: 0x0000000001989fb3 Faulting process id: 0x25d4 Faulting application start time: 0x01d795f5be3a354e Faulting application path: C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe Faulting module path: C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\PyQt5\Qt\bin\Qt5WebEngineCore.dll Report Id: 5284e8f0-d191-4d3d-a49f-a93dc84117b0 Faulting package full name: Faulting package-relative application ID: ---------------------------------------- Faulting application name: ChimeraX.exe, version: 1.3.0.0, time stamp: 0x611f7fb2 Faulting module name: Qt5WebEngineCore.dll, version: 5.15.2.0, time stamp: 0x5fad38ab Exception code: 0x80000003 Fault offset: 0x000000000014baff Faulting process id: 0x2940 Faulting application start time: 0x01d795f6781afa93 Faulting application path: C:\Program Files\ChimeraX 1.3.dev202108200941\bin\ChimeraX.exe Faulting module path: C:\Program Files\ChimeraX 1.3.dev202108200941\bin\lib\site-packages\PyQt5\Qt\bin\Qt5WebEngineCore.dll Report Id: c07bfcd1-8b63-4e87-9217-a1a77cc449f8 Faulting package full name: Faulting package-relative application ID: ---------------------------------------- As you can see, this happens on both of the most recent production versions of ChimeraX (1.2.5 and 1.1.0.0) as well as on the latest daily build (1.3.dev202108200941) as of 8/20/2021. Please let me know if there's any more information you need from us. Thanks, Mason -- Mason Long Information Technology Consultant ITS Client Technology Natural Resources Building 211C Humboldt State University 1 Harpst St. Arcata, CA 95521 (707) 826-5636 (email only for now) Create a new request for help at http://www.humboldt.edu/ithelp

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Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X
by Tom Goddard 18 Aug '21

18 Aug '21

Hi Matthias, When opening a script with the forEachFile option you can use $file in the script which will be replaced by the file basename. So in your script use fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save Tomo_fitted_$file_%d.pdb This is described in the forEachFile documentation https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> Tom > On Aug 18, 2021, at 7:57 AM, Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at> wrote: > > Dear Tom, > > Thank you again for the code for saving PDBs above a certain correlation score sing the fitmap command! I am now trying do use this on a large number of input volumes, and it’s working well except that I have a problem with naming the saved PDBs. So, my approach is the following: > > Open ChimeraX_Daily in no-gui mode > Type “open FitPDBinVolume.cxc foreach *.mrc” > The script FitPDBinVolume.cxc is very simple and looks like this: > > open 7apk > open /Volumes/matthias.vorlaender/Scripts/Chimera/fit_search.py > fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save /Volumes/plaschka/shared/data/em/Krios/20210616_endoTHO_tomo/Visualisation/mapping_back_using_imod/test/Tomo_fitted_%d.pdb > > What I would like to achieve is that the fitted PDBs are saved with a base name that matches that of the opened .mrc. Is there an easy way to do that? > > Thanks a lot in advance, > Best, > Matthias > > > From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of "Vorländer,Matthias Kopano via ChimeraX-users" <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Reply to: "Vorländer,Matthias Kopano" <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Date: Tuesday, 27. July 2021 at 07:40 > To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Cc: "chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X > > Hi Tom, > > Thanks so much, that's amazing! > > To be clear, I am not searching tomograms, I am searching artificial tomograms that contain perfect "molmaps" of my protein of interest, so they are free of noise. Trying this in Chimera gave very good fits when asking for for enough initial placement. > > Thanks a lot for your help, > Best, > Matthias > > Holen Sie sich Outlook für Android <https://aka.ms/AAb9ysg> > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, July 27, 2021 12:15:13 AM > To: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X > > Hi Matthias, > > You can run ChimeraX command scripts or Python scripts without a GUI, just start it at the shell with the "--nogui" option, for example > > chimerax --nogui mycommands.cxc > > I made some example Python code that runs fitmap search and saves PDB files for each unique fit with correlation over 0.9. > > https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html <https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html> > > I don't expect this to be a good way to search tomograms. It will be very inefficient. Template matching code designed for that problem is likely to work much better. Such code usually uses Fourier space methods to search all translations at once, so it can be much faster and more thorough. Even with that optimization it takes a long time to do the rotational search. > > Tom > > Example search of monomers in 14-mer GroEL. > > > > > > On Jul 25, 2021, at 9:05 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Dear all, > > I have a set of 100 “artificial” tomograms, each containing approx 100 copies of a simulated density map of my protein of interest. I would like to fit each tomogram with the PDB of my POI, and save copies for all fits with a correlation score > 90%. Using the fitmap command in Chimera and then manually selecting the fits that meet the criterium works, but takes quiet a long time for a larger amount of data. I wonder if this could be automated, and if somehow would be able me to put together a script (is it possible to execute such tasks in a non-gui way, by submitting it to a cluster so that it could be parallelized?). > > Thanks a lot in advance, > Best, > Matthias > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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Re: [chimerax-users] How to adjust chimeraX's loop display style?
by Elaine Meng 17 Aug '21

17 Aug '21

Hi Xiangan, Sorry no, there is no way to smooth the loops (coil) parts of a ribbon or cartoon. Currently only strands can be smoothed. By "smoothed" I mean that the path of the ribbon may not follow the CA atoms exactly, which can cause problems when the sidechains are displayed. In Chimera when the sidechains were displayed with ribbon, you could get unrealistically long or short CA-CB bonds. So in ChimeraX we decided it was more important to have an accurate CA-CB bond length when sidechains are displayed. In the helix and coil (loop) there is no smoothing option so the ribbon is exactly on the CA positions. Strands have a smoothing option turned on by default, because people expect them to be drawn as mostly straight, and if strands are not smoothed, they are very ripply. In ChimeraX when the strands are smoothed but sidechains are shown, the CA atoms that fall off the ribbon are shown with a connecting "tether" instead of stretching or shrinking the CA-CB bond artificially. This is discussed in the "cartoon" help, see the "smooth" for how to adjust strand smoothing and "cartoon tether": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> I investigated whether I could make a smoother representation with the "shape tube" command, but was unsuccessful. Sorry for the inconvenience -- I'm hoping that explaining the reasons might make it less annoying. :-) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2021, at 1:12 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > ChimeraX's default loop style shows very cursive. I like the way loop shows in chimera. > Is there any way to make chimeraX's loop display straighter? > Thanks, > Xiangan > > <image.png>

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Chimerax for Ubuntu 21.04
by jobiph 17 Aug '21

17 Aug '21

Dear all, thank you for your fast and thorough answers. I reinstalled lifbffi7 and libllvm6.0 and now Chimerax works. Thanks a lot! Kind regards Jonas

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Re: [chimerax-users] Chimerax for Ubuntu 21.04
by Gabriel Goetten 16 Aug '21

16 Aug '21

Hi, I was able to run chimeraX on ubuntu 21.04 by installing the following package https://answers.launchpad.net/ubuntu/hirsute/amd64/libllvm10/1:10.0.1-6 Then you just need to download chimerax of the following version Ubuntu 20.04 (Linux) 64-bit from their website (deb package). Gabriel

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Chimerax for Ubuntu 21.04
by jobiph 16 Aug '21

16 Aug '21

Dear all, is the current version of Chimera for Ubuntu (20.04) compatible with the 21.04 Ubuntu release? If i try to install the 20.04 version a weird dependency error pops up and I can't install the missing library because on the canonical website it states that this library is deprecated. Thank you for your help and kind regards Jonas

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All-numeric residue names
by Tristan Croll 16 Aug '21

16 Aug '21

Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287?

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ChimeraX-users August 2021